[Freesurfer] ROI Curvature

Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a st

Re: [Freesurfer] analyze format

Can you give us more detail? In particular, look at: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting doug Chacko Cherian wrote: Hello, I am having some trouble in running "Analyze" format images on freesurfer.Could someone please guide me on how to run images on this format.. THanx Chacko.

[Freesurfer] analyze format

Hello, I am having some trouble in running "Analyze" format images on freesurfer.Could someone please guide me on how to run images on this format.. THanx Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around h

Re: [Freesurfer] troubleshooting

Hi Amanda, What are the intensity values of the regions that are being left out? If they aren't near 110 then you should definitely use some control points. Where are the rh surfaces including some of the left hemisphere? Is it along the medial wall? Jenni On Wed, 24 May 2006, Amanda Dow

[Freesurfer] can we use mri_strip_skull with .mgz volumes?

Hi, I've noticed that mri_strip_skull and mri_make_bem_surfaces are not working with .mgz files. They look for COR-.info and fail if it doesn't exist. Best, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, S

Re: [Freesurfer] can we use mri_strip_skull with .mgz volumes?

we don't use them anymore. I think mri_watershed can create the bem surfaces if you give it the right command line. Bruce On Wed, 24 May 2006, Darren Weber wrote: Hi, I've noticed that mri_strip_skull and mri_make_bem_surfaces are not working with .mgz files. They look for COR-.info and fa

[Freesurfer] troubleshooting

I ran one of my brains through recon-all and the skull strip and talairach were normal. When I checked the white matter edits with tkmedit, the right hemisphere wm and pial surface lines are including some of the left hemisphere, and the right temporal lobes are not included as white matter or in t

Re: [Freesurfer] Reconstruction -> cortical maps without using Talairach transform

I think I see what you mean. But the answer is no, FreeSurfer will always resample to 256^3, 1mm, coronal. But you  can still use your ROIs, you just need to make a registration matrix first. Do this: tkregister2 --targ orig.mgz --mov rawavg.mgz --reg register.dat It is assumed that rawavg.m

Re: [Freesurfer] Reconstruction -> cortical maps without using Talairach transform

Doug, I think that you answered my question. We wanted to overlay some ROI files onto the freesurfer created surfaces, but the ROIs were made before we ran the images through freesurfer. So we wanted to make sure that we could keep the surfaces in the same space as the ROIs we created...is that

Re: [Freesurfer] Reconstruction -> cortical maps without using Talairach transform

What do you mean by "native space"? The reconstruction is not done in tal space. doug adam walczak wrote: Hello, I want to make cortical surface images that we will overlay with our own masks.  But we want to do this in native space.  So, I was wondering if it is possible to go thorugh the

[Freesurfer] Reconstruction -> cortical maps without using Talairach transform

Hello, I want to make cortical surface images that we will overlay with our own masks.  But we want to do this in native space.  So, I was wondering if it is possible to go thorugh the reconstruction process to make the surfaces without ever using the talairach transform and keeping everything in